Throttle discontinuity

During some test flights today we noticed some alarming behavior.

On several occasions, which I believe coincide with waypoints being completed the throttle control abruptly get set 0 zero for a short time. See 26:10.75 for an example. At the same instant commanded pitch an roll angles also momentarily become 0.

In all cases the system did recover correctly, but this is still scary. What is going on?